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arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays
2005
BMC Bioinformatics
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of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). ...
We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying ...
Conclusion We present arrayCGHbase, a versatile web based, platform independent data storage and analysis tool for processing microarray CGH data. ...
doi:10.1186/1471-2105-6-124
pmid:15910681
pmcid:PMC1173083
fatcat:o23fqjhs2vafnfykt5w3hyif7e
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
2011
Journal of Clinical Bioinformatics
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Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. ...
The FISH Oracle application and an installed demo web server are available at ...
In the following we will use the term array CGH (array comparative genomic hybridization) as a synonym for methods generating copy number data including classical array CGH tiling microarrays or SNP microarrays ...
doi:10.1186/2043-9113-1-20
pmid:21884636
pmcid:PMC3164613
fatcat:vjmj5wf6gba2vap3vpmce567t4
Array comparative genomic hybridization and flow cytometry analysis of spontaneous abortions and mors in utero samples
2009
BMC Medical Genetics
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For several decades chromosome analysis has been the golden standard to detect these genomic imbalances. A major drawback of this method is the requirement of short term cultures of fetal cells. ...
Karyotyping was unsuccessful in 28% of cases as compared to only two out of hundred samples with inconclusive results for combined array CGH and FCM analysis. ...
Acknowledgements We are grateful to the patients and their family for their cooperation. The authors wish to thank Ivy Jennes and Katrien Broekaert for expert technical assistance. ...
doi:10.1186/1471-2350-10-89
pmid:19751515
pmcid:PMC2753309
fatcat:hk6ucohrsndtzlwx6ykqoh3jga
CAPweb: a bioinformatics CGH array Analysis Platform
2006
Nucleic Acids Research
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The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. ...
CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visualization and biological interpretation ...
Funding to pay the Open Access publication charges for this article was provided by Institut Curie. ...
doi:10.1093/nar/gkl215
pmid:16845053
pmcid:PMC1538852
fatcat:zkirbuwc7nalldmovmbxc3has4
Low-grade chromosomal mosaicism in human somatic and embryonic stem cell populations
2014
Nature Communications
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Here we study the genetic content of 92 individual human cells, including fibroblasts, amniocytes and embryonic stem cells (hESCs), using single-cell array-based comparative genomic hybridization (aCGH ...
The recent development of high-resolution full-genome analysis methods applicable to single cells is providing new insights into genetic and cellular diversity. ...
Stem Cell Laboratory for the derivation and culture of the cell lines. ...
doi:10.1038/ncomms5227
pmid:24970340
fatcat:osgmsmhlijcppkgm24nb5yyjvq
CGHPRO -- a comprehensive data analysis tool for array CGH
2005
BMC Bioinformatics
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Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. ...
We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. ...
, Sarah Shoichet for reading the manuscript, Martin Vingron for fruitful discussions and the anonymous reviewers for their helpful comments. ...
doi:10.1186/1471-2105-6-85
pmid:15807904
pmcid:PMC1274268
fatcat:dai7bg4zcffjjnnd6le5wsgtpi
Scientific Poster Presentations
2018
Innovations (Philadelphia): technology and techniques in cardiothoracic and vascular surgery
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Methods and Materials. cDNA microarray expression profiling with over 17,000 probes, and array comparative genomic hybridization (aCGH) on 1Mb-spaced or full genomic tiling path BAC platforms, were used ...
Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of constitutional chromosomal aberrations is the application of microarray technology that is coming ...
doi:10.1097/imi.0000000000000475
pmid:29668500
fatcat:5nsrkts2obabzead6aqfueflva
Scientific Poster Presentations
2007
Cellular Oncology
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All samples contained >60% of tumour cells as assessed by pathological analysis. aCGH was performed in a 44K oligonucleotide Human Genome CGH Microarray platform from Agilent Technologies. ...
We aimed to characterize new genomic alterations in primary melanocytic lesions by using a high resolution CGH array platform. ...
Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of constitutional chromosomal aberrations is the application of microarray technology that is coming ...
doi:10.1155/2007/490242
doaj:bfd9d2a9659c4b6f94755e4d9ed1a380
fatcat:alhh6bfk6badjkr5hm6cc2vdsu
Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
2013
PLoS ONE
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Next we applied an integrated genomics analysis to prioritize MYCN down regulated genes mediated by MYCN driven miRNAs within regions of focal heterozygous or homozygous deletion. ...
Neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells. ...
Acknowledgments We would like to acknowledge Fanny De Vloed, Lies Vantomme, Justine Nuytens, Els De Smet, Anneleen Beckers, Jeroen Schacht, Kathleen Claes and Nathalie Goderis for their excellent technical ...
doi:10.1371/journal.pone.0052321
pmid:23308108
pmcid:PMC3537730
fatcat:3kswu6iimre3hhwtorqq3y3u6q
Human embryonic stem cells show low-grade microsatellite instability
2014
Molecular human reproduction
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An exception is the situation termed microsatellite instability (MSI), in which microsatellite loci change in size (Boland et al., 1998) . ...
Microsatellites are stretches of repetitive DNA sequence and are scattered throughout the human genome (Weber, 1990) . ...
Acknowledgements The authors acknowledge their colleagues from the HESC laboratory for the derivation and culture of the cell lines. ...
doi:10.1093/molehr/gau059
pmid:25082980
fatcat:4lsxfua7wbarrixosqsmugmhbi
A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies
2014
Oncogene
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Array comparative genome hybridization showed that chromosomal aberrations in LSL-MYCN;Dbh-iCre tumors were syntenic to those observed in human neuroblastomas. ...
expression and genomic make up. ...
This work was supported by the National Genome Research Network of the German Ministry for Education and Research (NGFNplus grant #PKN-01GS0894-6 to JHS, AE and AS), the 7th framework European Union project ...
doi:10.1038/onc.2014.269
pmid:25174395
pmcid:PMC4487199
fatcat:akr2jcsh7be65bqcfpkpmhhqd4
The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia
2014
Blood
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T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive form of leukemia that is mainly diagnosed in children and shows a skewed gender distribution toward males. ...
Interestingly, UTX mutations were exclusively present in male T-ALL patients and allelic expression analysis revealed that UTX escapes X-inactivation in female T-ALL lymphoblasts and normal T cells. ...
and Research Animal Resource Center for assistance with mouse experiments, and the Laboratory of Comparative Pathology for histologic analysis. ...
doi:10.1182/blood-2014-05-577270
pmid:25320243
pmcid:PMC4347284
fatcat:jdw5si5igndhndb22nxblz3day
Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells
2018
Stem Cell Reports
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ACKNOWLEDGMENTS The authors would like to acknowledge Lise Barbé for providing DNA samples from the VUBi004 lines. ...
The samples are hybridized on the microarray slide (4 3 44K Human Genome CGH Microarray, Agilent Technologies) for 24 hr. ...
The data were extracted using Agilent Feature Extraction software and analyzed with the ''ArrayCGHbase'' analysis platform (http://medgen.ugent.be/arrayCGHbasecmgg/) (Menten et al., 2005) . ...
doi:10.1016/j.stemcr.2018.05.007
pmid:29910126
pmcid:PMC6117474
fatcat:kw2tp33wuberlnumet74gxsm2q
A Novel t(8;14)(q24;q11) Rearranged Human Cell Line as a Model for Mechanistic and Drug Discovery Studies of NOTCH1-Independent Human T-Cell Leukemia
2018
Cells
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Altogether, this cell line may be a useful model system for dissecting the signaling pathways implicated in NOTCH1-independent T-ALL and for the screening of targeted anti-leukemia agents specific for ...
Identification of drug targets and mechanistic insights for this disease are still limited. ...
Scarparo for performing immunophenotypic analysis of cell lines and xenografts. ...
doi:10.3390/cells7100160
pmid:30304769
pmcid:PMC6209910
fatcat:bcvvsgafpvevxi3tjs6lwl3lza
PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia
2018
Journal of Experimental Medicine
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We thank Aaron Thorner, Paul Van Hummelen, and Matthew Ducar for assistance with targeted exome sequencing analysis. ...
We thank Jian Xu for SUZ12 shRNA hairpins, Tobias Neff and Scott Armstrong for Ezh2and Eed-floxed mice, Dario Altieri for gamitrinib, and Andrew Weng and David Weinstock for some of the patient-derived ...
To investigate underlying mechanisms, we began by applying targeted exome sequencing, array comparative genomic hybridization (CGH), and RNA sequencing analysis (RNA-seq) to all cases with sufficient available ...
doi:10.1084/jem.20180570
pmid:30404791
pmcid:PMC6279404
fatcat:qqjbjxt7nbd5vhdp2to5zsxnai